High-ranking member of the Sinaloa cartel cooperating with US. Photograph: Eduardo Verdugo/AP

The young Mexican drug lord Jesus Vicente Zambada Niebla made headlines three years ago when he claimed the United States government had protected his father's drug cartel in return for providing information against rival cartel members. Now, with the revelation this week that Zambada's legal team and the US attorney's office signed a secret plea agreement a year ago, he has struck a deal of his own.

It is, in effect, a cooperation agreement. With the stroke of a pen, the cartel insider who once vowed to put US undercover operations in Mexico on trial turned into an informant against the Sinaloa cartel of his powerful father, Ismael Zambada, a kingpin known simply as El Mayo.

Zambada, 39, was captured in 2009 in Mexico City by a special unit of the Mexican army, four hours after he met in a private room at the Sheraton Hotel with two agents from the Drug Enforcement Administration. He was extradited to Chicago in 2010 to face charges that he was the “logistical co-ordinator” for the Sinaloa cartel, overseeing shipments of cocaine and heroin by the ton from South and Central America through Mexico and into the United States.

Court documents from three years ago said the Sinaloa cartel had been given most favored status to continue to smuggle tons of illicit drugs into the US while its leaders were protected from arrest and prosecution at home. His defense strategy was clear: threaten to unravel the the US "war on drugs" in Mexico.

In part at least, that bold strategy has worked. Depending on his level of cooperation, prosecutors will ask that his inevitable life sentence be reduced to 10 years. Spokesmen with the DEA and the US attorney's office in Chicago declined to comment on the timing of the announcement.

In Mexico, however, the timing for the Sinaloa cartel could hardly be worse. The cartel is still reeling from the arrest of its leader, Joaquin "El Chapo" Guzman in February. Now Mayo Zambada, the former No 2 who is the logical choice to replace El Chapo, must compete for the loyalty of his predecessor's men while having to answer for the very public disloyalty of his own son. The Justice Department made the entire plea available for download on its website.

The government came to the negotiating table because Zambada posed an extraordinarily valuable source for information about the Sinaloa cartel, its associates and enemies. A plea agreement also prevents any further exposure of covert DEA operations in Mexico. Zambada, for his part, was at a disadvantage. Time and again his bold legal strategy had to contend with the Classified Information Procedures Act, a law invoked in cases such as his to balance the defendant's right to view evidence against the public's interest in nondisclosure.

Zambada also had to consider that his two main drug importers to the US, twin brothers Pedro and Margarito Flores, had agreed to testify against him. Between the two of them, the Flores twins estimated they had met in person with Zambada about 60 times. Pedro named Zambada as the second-ranking member of his father's organization, and could peg him to a delivery of 398kg of cocaine. Margarito had a recording of Zambada asking over the telephone about payment for twenty kilos of heroin.

In the end, the government turned a liability to its advantage. By dropping one drug charge and upholding the other, the government leaves Zambada the option to cooperate and go free in 10 years. He has already served four.

For more than three years, Zambada's case has bogged down in federal court as the defense argued for the release of sensitive documents pertaining to undercover operations in Mexico that the prosecution dismissed as a fishing expedition.

The case had barely budged until Thursday, when the judge revealed the existence of the plea agreement. The prosecution had requested in January that the document be unsealed, arguing that the original concerns for sealing it had “passed or have been remedied”. US district Judge Ruben Castillo obliged.

Zambada's future now depends on his willingness to inform on Mexican cartels, including his father's. Zambada waived his right to withdraw his plea or appeal any court decision. In return for his truthful and complete cooperation, the prosecution will ask the court limit his sentence to ten years. The government also pledged to provide for the safety of Zambada and his family against reprisals. There is even mention of steps to secure his legal stay in the US in the event of his release from custody. But if Zamabda's cooperation falls short of the government's expectations, he is out of cards to play.

Randall Samborn of the US attorney's office in Chicago declined to say where Zambada is being held. Zambada's name no longer appears in the public database of the Federal Bureau of Prisons.

The past year – Zambada's first as a government informant – was filled with misfortune for the Sinaloa cartel.

It's uncertain whether Zambada could have provided the government with the real-time intelligence needed to capture El Chapo or other Sinaloa cartel figures. Zambada lived in solitary confinement for a year in Mexico and two years in the US. And for five months in Chicago, he lived without sunlight or fresh air. All prison personnel below the rank of lieutenant with the exception of his counselor were barred from speaking to him.

What Zambada has to offer the government is his memory. According to the agreement, he knows which Mexican law enforcement officials took bribes. He knows the key players and the relationships that have stood the test of time. And if his memory serves him well, it just may be enough to convict the next Sinaloa cartel associate of his to stand trial in the US.